Hepatitis C Virus (HCV), the major cause of post-transfusion, community-acquired and cryptogenic non-A, non-B hepatitis (NANBH) (Choo et al., Br. Med. Bull. 46:423-441, 1990), is a persistent health threat worldwide, with more than one million new cases reported annually (Zein, Clin. Micro. Rev. 13:223-235, 2000). Over 170 million individuals are infected with HCV worldwide (see, e.g., Chevaliez et al., PLoS ONE 4:e8209, 2009.), and HCV infection is almost always chronic and persistent. The most severe consequences of HCV infection are chronic liver disease and death, and HCV infection is the primary impetus for liver transplantation in the United States (Zein, supra).
HCV is a positive strand single-stranded RNA virus approximately 10 kb long belonging to the Flaviviridae family (Zein, supra). There is considerable heterogeneity among isolates found in different geographic regions. These differences have been classified into multiple genotypes and subtypes. Although various different criteria have been used to characterize these genotypes, two principal modes of classification have been adopted. The more widely used of these was created by Peter Simmonds and uses Arabic numerals to denote different genotypes and latin letters for subtypes, e.g., type 1a, 1b, 2a, etc. (reviewed in Simmonds, Hepatol., 21:570-83, 1995; Simmonds, Hepatol. 31 Suppl 1:54-60, 1999). According to this system, genotypes 1-3 are the prevalent types found in North America, Europe, and Japan, and the remaining types are found at various frequencies in parts of Asia and Africa. Thus in some instances HCV genotype may be of epidemiological importance, for example in determining the etiology of infection.
Efforts have been undertaken to elucidate the clinical significance of different genotypes. Some studies suggest that infections of type 1, in particular type 1b, may be associated with more severe disease and earlier recurrence (Zein et al., Liver Transplant. Surg. 1:354-357, 1995; Gordon et al., Transplantation 63:1419-1423, 1997). Certain studies have also indicated that genotypes other than type 1 may respond more favorably to various treatments, e.g. interferon (McHutchison et al., N. Engl. J. Med., 339:1485-1492, 1998). It has been suggested that determination of HCV genotype in combination with other diagnostic markers, such as viral load, may be of value in arriving at disease prognoses (Zein, supra), and determining the course of treatment (National Institutes of Health Consensus Development Conference Statement; Management of Hepatitis C: 2002; Jun. 10-11, 2002).
Although HCV genotype 1 is generally considered as a homogeneous group, there are biological differences between the different subtypes of HCV genotype 1, which are related to differences in their nucleotide and amino acid sequences. For example, differences between subtype 1a and 1b (by far the most frequently encountered genotype 1 subtypes in clinical practice) include different efficacies of antiviral drugs and different resistance profiles to such drugs. (Chevaliez et al., PLoS ONE 4:e8209, 2009.) Several HCV inhibitors appear to have selective activity against different HCV genotype 1 subtypes, both in vitro and in vivo. (Id.) For example, differences have been observed in vitro with NS3/4A protease inhibitors, non-nucleoside inhibitors of HCV RdRp, and NS5A inhibitors (Erhardt et al., Antivir. Ther. 14:23-32, 2009; Jiang et al., J. Hepatol. 50 (suppl. 1):56, 2009; Liang et al., Gastroenterology 135:1710-1718, 2008; Nettles et al., Hepatology 48 (suppl. 1):1025A, 2008; Thompson et al., J. Hepatol. 50 (suppl. 1):537, 2009).
Correct identification of HCV subtypes 1a and 1b is critical in clinical trials assessing new HCV drugs in order to correctly stratify and interpret efficacy and resistance data. In addition, such genotype identification is likely to become increasingly important in clinical practice to select HCV inhibitor treatment according to HCV genotype 1 subtype. (See Chevaliez et al., supra.)
Accordingly, there is a need for compositions and methods for determining genotype information for HCV type 1 so as to correctly identify mutations or single nucleotide polymorphisms (SNPs) associated with treatment efficacy or resistance, including the correct identification of HCV subtypes 1a and 1b. The present invention meets these and other needs.